ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for PRKACA

Gene summary

Gene information	Gene symbol	PRKACA
	Gene ID	5566
	Gene name	protein kinase cAMP-activated catalytic subunit alpha
	Synonyms	PKACA\|PPNAD4
	Cytomap	19p13.12
	Type of gene	protein-coding
	Description	cAMP-dependent protein kinase catalytic subunit alphaPKA C-alphaprotein kinase A catalytic subunitprotein kinase, cAMP-dependent, alpha catalytic subunitprotein kinase, cAMP-dependent, catalytic, alpha
	Modification date	20200327
	UniProtAcc	A0A024R7J0, K7EMV1, K7ENJ5, K7ERP6, P17612, Q15136,
	Context

Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Gene	GO ID	GO term	PubMed ID
PRKACA	GO:0006397	mRNA processing	17594903
PRKACA	GO:0006468	protein phosphorylation	12475942
PRKACA	GO:0018105	peptidyl-serine phosphorylation	10805756\|11029056
PRKACA	GO:0034605	cellular response to heat	21085490
PRKACA	GO:0045667	regulation of osteoblast differentiation	19949837
PRKACA	GO:0061136	regulation of proteasomal protein catabolic process	17565987
PRKACA	GO:0071333	cellular response to glucose stimulus	19949837
PRKACA	GO:2000810	regulation of bicellular tight junction assembly	15905176

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Gene structures and expression levels for PRKACA

Skipped exons in the ROSMAP, MSBB, and Mayo based on Ensembl gene isoform structure.
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

ENSG00000072062

Differentially expressed gene analysis across multiple brain tissues between AD and control.

Tissue type

DEG direction

Base mean exp.

log2FC(AD/control)

P-value

Adj. p-value

Differentially expressed isoform analysis across multiple brain tissues between AD and control.

Tissue type

DEG direction

ENST

Transcript info.

Base mean exp.

log2FC(AD/control)

P-value

Adjc. p-value

Landscape of isoform expressions across multiple brain tissues between AD and control.

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Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for PRKACA

Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap).

All exon skipping events in AD cohorts.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon
exon_skip_207234	chr19	14093219:14093237:14093628:14093792:14097361:14097483	14093628:14093792
exon_skip_213026	chr19	14097579:14097674:14097764:14097890:14100826:14100908	14097764:14097890
exon_skip_261863	chr19	14097764:14097890:14100826:14100908:14102816:14102914	14100826:14100908
exon_skip_36150	chr19	14093043:14093237:14093628:14093792:14097361:14097483	14093628:14093792
exon_skip_56246	chr19	14093050:14093237:14093628:14093792:14097361:14097483	14093628:14093792
exon_skip_57326	chr19	14097361:14097483:14097579:14097674:14097764:14097890	14097579:14097674
exon_skip_57545	chr19	14100826:14100908:14102816:14102914:14106760:14106860	14102816:14102914

Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control.

Exon skipping information

Tissue type

Avg(PSIs) in AD

Avg(PSIs) in control

Difference (PSI)

Adj. p-value

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Open reading frame (ORF) annotation in the exon skipping event for PRKACA

Open reading frame (ORF) of individual exon skipping events in ROSMAP based on the Ensembl gene structure combined from isoforms.

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000308677	14097764	14097890	Frame-shift
ENST00000308677	14093628	14093792	In-frame
ENST00000308677	14097579	14097674	In-frame
ENST00000308677	14102816	14102914	In-frame

Open reading frame (ORF) of individual exon skipping events in MSBB based on the Ensembl gene structure combined from isoforms.

ENST

Start of skipped exon

End of skipped exon

ORF

Open reading frame (ORF) of individual exon skipping events in Mayo based on the Ensembl gene structure combined from isoforms.

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000308677	14097764	14097890	Frame-shift
ENST00000308677	14100826	14100908	Frame-shift
ENST00000308677	14093628	14093792	In-frame
ENST00000308677	14097579	14097674	In-frame
ENST00000308677	14102816	14102914	In-frame

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Infer the effects of exon skipping event on protein functional features for PRKACA

p-ENSG00000072062_img4.png
boxplot

Loci of skipped exons in ROSMAP across genomic, transcript, and protein sequence levels of In-frame cases.

ENST	Length of mRNA	Length of AA seq.	Genomic start	Genomic end	mRNA start	mRNA end	AA start	AA end
ENST00000308677	2694	351	14102816	14102914	435	532	79	111
ENST00000308677	2694	351	14097579	14097674	744	838	182	213
ENST00000308677	2694	351	14093628	14093792	963	1126	255	309

Loci of skipped exons in MSBB across genomic, transcript, and protein sequence levels of In-frame cases.

ENST

Length of mRNA

Length of AA seq.

Genomic start

Genomic end

mRNA start

mRNA end

AA start

AA end

Loci of skipped exons in Mayo across genomic, transcript, and protein sequence levels of In-frame cases.

ENST	Length of mRNA	Length of AA seq.	Genomic start	Genomic end	mRNA start	mRNA end	AA start	AA end
ENST00000308677	2694	351	14102816	14102914	435	532	79	111
ENST00000308677	2694	351	14097579	14097674	744	838	182	213
ENST00000308677	2694	351	14093628	14093792	963	1126	255	309

Lost protein functional features of individual exon skipping events in ROSMAP.

UniProt acc.	Start of exon skipping (AA)	End of exon skipping (AA)	Protein feature start (AA)	Protein feature end (AA)	Category of protein feature	Description of feature
P17612	79	111	107	112	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4WB8
P17612	79	111	2	351	Chain	ID=PRO_0000086052;Note=cAMP-dependent protein kinase catalytic subunit alpha
P17612	79	111	44	298	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
P17612	79	111	77	82	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4WB8
P17612	79	111	86	98	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4WB8
P17612	79	111	96	96	Mutagenesis	Note=Enhanced basal kinase activity%3B when associated with R-48%2C L-121%2C A-124%2C K-182 and A-184. L->Q;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21774789;Dbxref=PMID:21774789
P17612	182	213	181	183	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4WB8
P17612	182	213	212	214	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5IZJ
P17612	182	213	2	351	Chain	ID=PRO_0000086052;Note=cAMP-dependent protein kinase catalytic subunit alpha
P17612	182	213	44	298	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
P17612	182	213	186	188	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4UJ2
P17612	182	213	203	205	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4WB8
P17612	182	213	208	211	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4WB8
P17612	182	213	196	196	Modified residue	Note=Phosphothreonine;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12372837;Dbxref=PMID:12372837
P17612	182	213	198	198	Modified residue	Note=Phosphothreonine%3B by PDPK1;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:12372837,ECO:0000269\|PubMed:16765046,ECO:0000269\|PubMed:20137943,ECO:0000269\|PubMed:20481595,EC
P17612	182	213	182	182	Mutagenesis	Note=Enhanced basal kinase activity%3B when associated with R-48%2C Q-96%2C L-121%2C A-124 and A-184. Q->K;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21774789;Dbxref=PMID:21774789
P17612	182	213	184	184	Mutagenesis	Note=Enhanced basal kinase activity%3B when associated with R-48%2C Q-96%2C L-121%2C A-124 and K-182. T->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21774789;Dbxref=PMID:21774789
P17612	182	213	195	195	Mutagenesis	Note=No phosphorylation. R->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12372837;Dbxref=PMID:12372837
P17612	182	213	201	201	Mutagenesis	Note=No phosphorylation. G->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12372837;Dbxref=PMID:12372837
P17612	182	213	202	202	Mutagenesis	Note=No phosphorylation. T->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12372837;Dbxref=PMID:12372837
P17612	182	213	205	205	Mutagenesis	Note=Loss of allosteric regulation. Y->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:18178622;Dbxref=PMID:18178622
P17612	182	213	206	206	Natural variant	ID=VAR_071707;Note=In PPNAD4%3B somatic mutation%3B the mutation results in cAMP-independent basal protein kinase activity and constitutive activation of protein kinase A. L->R;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:000
P17612	255	309	2	351	Chain	ID=PRO_0000086052;Note=cAMP-dependent protein kinase catalytic subunit alpha
P17612	255	309	44	298	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
P17612	255	309	299	351	Domain	Note=AGC-kinase C-terminal
P17612	255	309	264	273	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4WB8
P17612	255	309	290	293	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4WB8
P17612	255	309	296	298	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4WB8
P17612	255	309	303	307	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4WB8
P17612	255	309	264	264	Natural variant	ID=VAR_040593;Note=S->C;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17344846;Dbxref=dbSNP:rs35635531,PMID:17344846
P17612	255	309	278	280	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4WB8
P17612	255	309	282	284	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5IZF
P17612	255	309	286	289	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4WB8

Lost protein functional features of individual exon skipping events in MSBB.

UniProt acc.

Start of exon skipping (AA)

End of exon skipping (AA)

Protein feature start (AA)

Protein feature end (AA)

Category of protein feature

Description of feature

Lost protein functional features of individual exon skipping events in Mayo.

UniProt acc.	Start of exon skipping (AA)	End of exon skipping (AA)	Protein feature start (AA)	Protein feature end (AA)	Category of protein feature	Description of feature
P17612	79	111	107	112	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4WB8
P17612	79	111	2	351	Chain	ID=PRO_0000086052;Note=cAMP-dependent protein kinase catalytic subunit alpha
P17612	79	111	44	298	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
P17612	79	111	77	82	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4WB8
P17612	79	111	86	98	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4WB8
P17612	79	111	96	96	Mutagenesis	Note=Enhanced basal kinase activity%3B when associated with R-48%2C L-121%2C A-124%2C K-182 and A-184. L->Q;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21774789;Dbxref=PMID:21774789
P17612	182	213	181	183	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4WB8
P17612	182	213	212	214	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5IZJ
P17612	182	213	2	351	Chain	ID=PRO_0000086052;Note=cAMP-dependent protein kinase catalytic subunit alpha
P17612	182	213	44	298	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
P17612	182	213	186	188	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4UJ2
P17612	182	213	203	205	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4WB8
P17612	182	213	208	211	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4WB8
P17612	182	213	196	196	Modified residue	Note=Phosphothreonine;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12372837;Dbxref=PMID:12372837
P17612	182	213	198	198	Modified residue	Note=Phosphothreonine%3B by PDPK1;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:12372837,ECO:0000269\|PubMed:16765046,ECO:0000269\|PubMed:20137943,ECO:0000269\|PubMed:20481595,EC
P17612	182	213	182	182	Mutagenesis	Note=Enhanced basal kinase activity%3B when associated with R-48%2C Q-96%2C L-121%2C A-124 and A-184. Q->K;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21774789;Dbxref=PMID:21774789
P17612	182	213	184	184	Mutagenesis	Note=Enhanced basal kinase activity%3B when associated with R-48%2C Q-96%2C L-121%2C A-124 and K-182. T->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21774789;Dbxref=PMID:21774789
P17612	182	213	195	195	Mutagenesis	Note=No phosphorylation. R->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12372837;Dbxref=PMID:12372837
P17612	182	213	201	201	Mutagenesis	Note=No phosphorylation. G->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12372837;Dbxref=PMID:12372837
P17612	182	213	202	202	Mutagenesis	Note=No phosphorylation. T->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12372837;Dbxref=PMID:12372837
P17612	182	213	205	205	Mutagenesis	Note=Loss of allosteric regulation. Y->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:18178622;Dbxref=PMID:18178622
P17612	182	213	206	206	Natural variant	ID=VAR_071707;Note=In PPNAD4%3B somatic mutation%3B the mutation results in cAMP-independent basal protein kinase activity and constitutive activation of protein kinase A. L->R;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:000
P17612	255	309	2	351	Chain	ID=PRO_0000086052;Note=cAMP-dependent protein kinase catalytic subunit alpha
P17612	255	309	44	298	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
P17612	255	309	299	351	Domain	Note=AGC-kinase C-terminal
P17612	255	309	264	273	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4WB8
P17612	255	309	290	293	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4WB8
P17612	255	309	296	298	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4WB8
P17612	255	309	303	307	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4WB8
P17612	255	309	264	264	Natural variant	ID=VAR_040593;Note=S->C;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17344846;Dbxref=dbSNP:rs35635531,PMID:17344846
P17612	255	309	278	280	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4WB8
P17612	255	309	282	284	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5IZF
P17612	255	309	286	289	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4WB8

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3'-UTR located exon skipping events that lost miRNA binding sites in PRKACA

3'-UTR exon skipping evnets lost miRNA binding.

Tissue type

ENST

Exon skip start

Exon skip end

microRNA

Binding site by TargetScan

Binding type by TargetScan

Bdinding site by miRanda

Score of miRanda

Energy by miRanda

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SNVs in the skipped exons for PRKACA

- Differential PSIs between mutated versus non-mutated samples.

- Depth of Coverage in the skipped exon of the mutated samples.

- Sashimi plot in the skipped exon of the mutated samples.

- Non-synonymous mutations located in the skipped exons.

Cancer type

Sample

ESID

Skipped exon start

Skipped exon end

Mutation start

Mutation end

Mutation type

Reference seq

Mutation seq

AAchange

- Non-synonymous mutations located in the skipped exons in CCLE.

Sample

Skipped exon start

Skipped exon end

Mutation start

Mutation end

Mutation type

Reference seq

Mutation seq

AAchange

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AD stage-associated exon skippint events for PRKACA

Associated exon skipping events with Braak staging or Clinical Dementia Rating (CDR).

AD stage info

Cohort

Tissue

SE id

Coefficient

P-value

Chromosome

Strand

E1 start

E1 end

Skipped start

Skipped end

E2 start

E2 end

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PRKACA

sQTL information located at the skipped exons.

Tissue type

Exon skip ID

SNP id

Location

P-value

FDR

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Correlation with RNA binding proteins (RBPs) for PRKACA

Correlated RBP and related information.

Tissue type

RBP name

Exon skip ID

Correlation coeifficient

P-value

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RelatedDrugs for PRKACA

Approved drugs targeting this gene.
(DrugBank Version 5.1.0 2018-04-02)

UniProtAcc	DrugBank ID	Drug name	Drug activity	Drug type	Drug status
P17612	approved\|investigational	DB12010	Fostamatinib	small molecule	P17612

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RelatedDiseases for PRKACA

Diseases associated with this gene.
(DisGeNet 4.0)

Gene

Disease ID

Disease name

# pubmeds

Source

	Gene summary
	Gene structures and expression levels
	Exon skipping events with PSIs in RPSMAP, MSBB, and Mayo
	Open reading frame (ORF) annotation in the exon skipping event
	Exon skipping events in the canonical protein sequence
	3'-UTR located exon skipping events lost miRNA binding sites
	SNVs in the skipped exons with depth of coverage
	AD stage-associated exon skipping events
	Splicing Quantitative Trait Loci (sQTLs) in the skipped exons
	Correlation with RNA binding proteins (RBPs)
	Related drugs with this gene
	Related diseases with this gene

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Gene summary for PRKACA

Gene structures and expression levels for PRKACA

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for PRKACA

Open reading frame (ORF) annotation in the exon skipping event for PRKACA

Infer the effects of exon skipping event on protein functional features for PRKACA

3'-UTR located exon skipping events that lost miRNA binding sites in PRKACA

SNVs in the skipped exons for PRKACA

AD stage-associated exon skippint events for PRKACA

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PRKACA

Correlation with RNA binding proteins (RBPs) for PRKACA

RelatedDrugs for PRKACA

RelatedDiseases for PRKACA